Expediting model selection for Support Vector Machines based on data reduction. - Yu-Yen Ou; Chien-Yu Chen 001; Shien-Ching Hwang; Yen-Jen Oyang (SMC, 2003)

A novel radial basis function network classifier with centers set by hierarchical clustering. - Yu-Yen Ou; Yen-Jen Oyang; Chien-Yu Chen 001 (IJCNN, 2005)

Data classification with a relaxed model of variable kernel density estimation. - Yen-Jen Oyang; Yu-Yen Ou; Shien-Ching Hwang; Chien-Yu Chen 001; Darby Tien-Hao Chang (IJCNN, 2005)

Data classification with radial basis function networks based on a novel kernel density estimation algorithm. - Yen-Jen Oyang; Shien-Ching Hwang; Yu-Yen Ou; Chien-Yu Chen 001; Zhi-Wei Chen (IEEE Trans. Neural Networks, 2005)

A Study of Supervised Learning with Multivariate Analysis on Unbalanced Datasets. - Yu-Yen Ou; Hao-Geng Hung; Yen-Jen Oyang (IJCNN, 2006)

Expediting Model Selection for Support Vector Machines Based on an Advanced Data Reduction Algorithm. - Yu-Yen Ou; Guan-Hau Chen; Yen-Jen Oyang (PRICAI, 2006)

Protein disorder prediction by condensed PSSM considering propensity for order or disorder. - Chung-Tsai Su; Chien-Yu Chen 001; Yu-Yen Ou (BMC Bioinform., 2006)

Enhancing Protein Disorder Detection by Refined Secondary Structure Prediction. - Chung-Tsai Su; Tong-Ming Hsu; Chien-Yu Chen 001; Yu-Yen Ou; Yen-Jen Oyang (BIRD, 2007)

Prediction of Protein Secondary Structures with a Novel Kernel Density Estimator. - Yen-Jen Oyang; Darby Tien-Hao Chang; Yu-Yen Ou; Hao-Geng Hung; Chien-Yu Chen 001 (MLMTA, 2007)

Using Efficient RBF Network to Identify Interface Residues Based on PSSM Profiles and Biochemical Properties. - Yu-Yen Ou; Shu-An Chen; Chung-Lu Shao; Hao-Geng Hung (PRIB, 2007)

TMBETADISC-RBF: Discrimination of beta-barrel membrane proteins using RBF networks and PSSM profiles. - Yu-Yen Ou; M. Michael Gromiha; Shu-An Chen; Makiko Suwa (Comput. Biol. Chem., 2008)

Using Efficient RBF Networks to Classify Transport Proteins Based on PSSM Profiles and Biochemical Properties. - Yu-Yen Ou; Shu-An Chen (IWANN (1), 2009)

Topology Prediction of alpha-Helical and beta-Barrel Transmembrane Proteins Using RBF Networks. - Shu-An Chen; Yu-Yen Ou; M. Michael Gromiha (ICIC (1), 2010)

Incorporating significant amino acid pairs to identify O-linked glycosylation sites on transmembrane proteins and non-transmembrane proteins. - Shu-An Chen; Tzong-Yi Lee; Yu-Yen Ou (BMC Bioinform., 2010)

Prediction of membrane spanning segments and topology in beta-barrel membrane proteins at better accuracy. - Yu-Yen Ou; Shu-An Chen; M. Michael Gromiha (J. Comput. Chem., 2010)

Prediction of transporter targets using efficient RBF networks with PSSM profiles and biochemical properties. - Shu-An Chen; Yu-Yen Ou; Tzong-Yi Lee; M. Michael Gromiha (Bioinform., 2011)

Bioinformatics approaches for functional annotation of membrane proteins. - M. Michael Gromiha; Yu-Yen Ou (Briefings Bioinform., 2014)

Using Deep Learning with Position Specific Scoring Matrices to Identify Efflux Proteins in Membrane and Transport Proteins. - Semmy Wellem Taju; Nguyen-Quoc-Khanh Le; Yu-Yen Ou (BIBE, 2016)

Prediction of FAD binding sites in electron transport proteins according to efficient radial basis function networks and significant amino acid pairs. - Nguyen-Quoc-Khanh Le; Yu-Yen Ou (BMC Bioinform., 2016)

Incorporating efficient radial basis function networks and significant amino acid pairs for predicting GTP binding sites in transport proteins. - Nguyen-Quoc-Khanh Le; Yu-Yen Ou (BMC Bioinform., 2016)

Incorporating deep learning with convolutional neural networks and position specific scoring matrices for identifying electron transport proteins. - Nguyen-Quoc-Khanh Le; Quang-Thai Ho; Yu-Yen Ou (J. Comput. Chem., 2017)

DeepEfflux: a 2D convolutional neural network model for identifying families of efflux proteins in transporters. - Semmy Wellem Taju; Trinh-Trung-Duong Nguyen; Nguyen-Quoc-Khanh Le; Rosdyana Mangir Irawan Kusuma; Yu-Yen Ou (Bioinform., 2018)

Incorporating post translational modification information for enhancing the predictive performance of membrane transport proteins. - Nguyen-Quoc-Khanh Le; Green Arther Sandag; Yu-Yen Ou (Comput. Biol. Chem., 2018)

Using Deep Learning Neural Networks and Candlestick Chart Representation to Predict Stock Market. - Rosdyana Mangir Irawan Kusuma; Trang-Thi Ho; Wei-Chun Kao; Yu-Yen Ou; Kai-Lung Hua (CoRR, 2019)

Using two-dimensional convolutional neural networks for identifying GTP binding sites in Rab proteins. - Nguyen-Quoc-Khanh Le; Quang-Thai Ho; Yu-Yen Ou (J. Bioinform. Comput. Biol., 2019)

DeepIon: Deep learning approach for classifying ion transporters and ion channels from membrane proteins. - Semmy Wellem Taju; Yu-Yen Ou (J. Comput. Chem., 2019)

A Self-Relevant CNN-SVM Model for Problem Classification in K-12 Question-Driven Learning. - Eric Hsiao-Kuang Wu; Sung-En Chen; Jhao-Jhong Liu; Yu-Yen Ou; Min-Te Sun (IEEE Access, 2020)

Advantages and Constraints of a Hybrid Model K-12 E-Learning Assistant Chatbot. - Eric Hsiao-Kuang Wu; Chun-Han Lin; Yu-Yen Ou; Chen-Zhong Liu; Wei-Kai Wang; Chi-Yun Chao (IEEE Access, 2020)

DeepETC: A deep convolutional neural network architecture for investigating and classifying electron transport chain's complexes. - Nguyen-Quoc-Khanh Le; Quang-Thai Ho; Edward Kien Yee Yapp; Yu-Yen Ou; Hui-Yuan Yeh (Neurocomputing, 2020)

A transformer architecture based on BERT and 2D convolutional neural network to identify DNA enhancers from sequence information. - Nguyen-Quoc-Khanh Le; Quang-Thai Ho; Trinh-Trung-Duong Nguyen; Yu-Yen Ou (Briefings Bioinform., 2021)

Addressing data imbalance problems in ligand-binding site prediction using a variational autoencoder and a convolutional neural network. - Trinh-Trung-Duong Nguyen; Duc-Khanh Nguyen; Yu-Yen Ou (Briefings Bioinform., 2021)

DeepSIRT: A deep neural network for identification of sirtuin targets and their subcellular localizations. - Syed Muazzam Ali Shah; Semmy Wellem Taju; Bongani Brian Dlamini; Yu-Yen Ou (Comput. Biol. Chem., 2021)

ActTRANS: Functional classification in active transport proteins based on transfer learning and contextual representations. - Semmy Wellem Taju; Syed Muazzam Ali Shah; Yu-Yen Ou (Comput. Biol. Chem., 2021)

FAD-BERT: Improved prediction of FAD binding sites using pre-training of deep bidirectional transformers. - Quang-Thai Ho; Trinh-Trung-Duong Nguyen; Nguyen-Quoc-Khanh Le; Yu-Yen Ou (Comput. Biol. Medicine, 2021)

Incorporating a transfer learning technique with amino acid embeddings to efficiently predict N-linked glycosylation sites in ion channels. - Trinh-Trung-Duong Nguyen; Nguyen-Quoc-Khanh Le; The-Anh Tran; Dinh-Minh Pham; Yu-Yen Ou (Comput. Biol. Medicine, 2021)

TRP-BERT: Discrimination of transient receptor potential (TRP) channels using contextual representations from deep bidirectional transformer based on BERT. - Syed Muazzam Ali Shah; Yu-Yen Ou (Comput. Biol. Medicine, 2021)

GT-Finder: Classify the family of glucose transporters with pre-trained BERT language models. - Syed Muazzam Ali Shah; Semmy Wellem Taju; Quang-Thai Ho; Trinh-Trung-Duong Nguyen; Yu-Yen Ou (Comput. Biol. Medicine, 2021)

mCNN-ETC: identifying electron transporters and their functional families by using multiple windows scanning techniques in convolutional neural networks with evolutionary information of protein sequences. - Quang-Thai Ho; Nguyen-Quoc-Khanh Le; Yu-Yen Ou (Briefings Bioinform., 2022)

Use Chou's 5-Steps Rule With Different Word Embedding Types to Boost Performance of Electron Transport Protein Prediction Model. - Trinh-Trung-Duong Nguyen; Quang-Thai Ho; Nguyen-Quoc-Khanh Le; Van-Dinh Phan; Yu-Yen Ou (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

An Extensive Examination of Discovering 5-Methylcytosine Sites in Genome-Wide DNA Promoters Using Machine Learning Based Approaches. - Trinh-Trung-Duong Nguyen; The-Anh Tran; Nguyen-Quoc-Khanh Le; Dinh-Minh Pham; Yu-Yen Ou (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

DeepPLM_mCNN: An approach for enhancing ion channel and ion transporter recognition by multi-window CNN based on features from pre-trained language models. - Van-The Le; Muhammad-Shahid Malik; Yi-Hsuan Tseng; Yu-Cheng Lee; Cheng-I Huang; Yu-Yen Ou (Comput. Biol. Chem., 2024)

MCNN_MC: Computational Prediction of Mitochondrial Carriers and Investigation of Bongkrekic Acid Toxicity Using Protein Language Models and Convolutional Neural Networks. - Muhammad-Shahid Malik; Yan-Yun Chang; Yu-Chen Liu 009; Van-The Le; Yu-Yen Ou (J. Chem. Inf. Model., 2024)

Anti-Drugs Chatbot: Chinese BERT-Based Cognitive Intent Analysis. - Jui-Hsuan Lee; Eric Hsiao-Kuang Wu; Yu-Yen Ou; Yueh-Che Lee; Cheng-Hsun Lee; Chia-Ru Chung (IEEE Trans. Comput. Soc. Syst., 2024)

mCNN-GenEfflux: enhanced predicting Efflux protein and their super families by using generative proteins combined with multiple windows convolution neural networks. - Muhammad Hussain; Yu-Yen Ou; Quang-Thai Ho (Comput. Biol. Chem., 2025)

ATP_mCNN: Predicting ATP binding sites through pretrained language models and multi-window neural networks. - Van-The Le; Muhammad-Shahid Malik; Yi-Jing Lin; Yu-Chen Liu 009; Yan-Yun Chang; Yu-Yen Ou (Comput. Biol. Medicine, 2025)

CaBind_MCNN: Identifying Potential Calcium Channel Blocker Targets by Predicting Calcium-Binding Sites in Ion Channels and Ion Transporters Using Protein Language Models and Multiscale Feature Extraction. - Yan-Yun Chang; Yu-Chen Liu 009; Wei-En Jhang; Sin-Siang Wei; Yu-Yen Ou (J. Chem. Inf. Model., 2025)

RAG_MCNNIL6: A Retrieval-Augmented Multi-Window Convolutional Network for Accurate Prediction of IL-6 Inducing Epitopes. - Cheng-Che Chuang; Yu-Chen Liu 009; Wei-En Jhang; Sin-Siang Wei; Yu-Yen Ou (J. Chem. Inf. Model., 2025)

RTK_RAG: Leveraging Retrieval Augmented Generation with Multi-Window Convolutional Neural Networks for Superior ATP Binding Site Prediction in Receptor Tyrosine Kinases. - Sin-Siang Wei; Wei-En Jhang; Yu-Chen Liu 009; Cheng-Che Chuang; Yu-Yen Ou (J. Chem. Inf. Model., 2025)